Modification of DNA methylation marks in plants

Phenotypic variation in higher eukaryotes has been found to be associated with different epigenetic states, some of which are associated with defined DNA methylation patterns. In this study, over-expressions of different forms of DNA METHYLTRANSFERASE1 (MET1), with and without catalytic sites and SAM binding domains, were used to alter the epigenetic states of potential target genes and therefore cause epigenetic variation in plants. The DNA methylation is mediated by the addition of a methyl group obtained from S-adenosylmethionone (SAM) to the carbon 5 of a cytosine residue. In plants, it involves de novo and maintenance of methylation in CG, CHG and CHH (H representing A, C or T) contexts catalysed by three classes of methyltransferases, namely METHYLTRANSFERASE 1 (MET1), CHROMOMETHYLTRANSFERASE 3 (CMT3), and DOMAIN-REARRANGED METHYLTRANSFERASE 2 (DRM2). De novo methylation in all sequence contexts is carried out via DRM2 as part of the RNA-directed DNA methylation (RdDM) pathway, while maintenance of CG and CHG methylation are catalysed by MET1 and CMT3, respectively. Phenotypic analysis of the Arabidopsis transformants of MET1 with and without catalytic sites (namely, the METo A1 and METo I1 lines) revealed a reduction in the primary root length in all lines and delayed germination in some of the line. In contrast, Arabidopsis transformants of MET1 without catalytic sites and SAM-binding domains (namely, the MSM line) lack the phenotypes that were observed in the METo lines. Root transcriptome analysis revealed increased expression of genes encoding transposable elements, non-coding RNAs and proteins. These findings in this study may form a foundation for future research to identify epigenetic control of specific target gene responsible for the root phenotype